Hi Chris
I use a gravel tidy or soil retainer, the type of mesh used for greenhouse shading and place the sand/gravel cap on top.
You can buy it from Amazon or usually garden centres.
http://www.amazon.co.uk/Gardman-Greenho ... 520&sr=8-3
It is very effective in partitioning the soil from the gravel/sand cap, and the disturbance from re-scaping is minimal.
Believe it or not once soil becomes saturated I have found that it is pretty hard to disturb anyway; that is if it's capped with something else. Even without a soil retainer all I get is a bit of very fine particle turbitiy, in fact the one and only Gucci substrate I've used has given me more problems in terms of re-scaping mess. Either way, a filter with a good turnover soon clears it all up.
But you don't have to just use sand or gravel to cap, you can do what Alastair has done in his chocolate puddle and use a Gucci substrate, or whatever takes your fancy, as long as the grain size is around a minimum of 2-3mm and is conducive to water movement and therefore gas and nutrient exchange, all is good.
But this, and much more, will be explained in next months issue of PFK